/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Hashtable;
+import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
@SuppressWarnings("serial")
public class AnnotationColourChooser extends AnnotationRowFilter
{
+ private static final int ONETHOUSAND = 1000;
- ColourSchemeI oldcs;
+ private ColourSchemeI oldcs;
- Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+ private JButton defColours;
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
+ private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
- JComboBox<String> annotations;
+ private JCheckBox useOriginalColours = new JCheckBox();
- JButton defColours = new JButton();
+ private JPanel minColour = new JPanel();
- JPanel jPanel1 = new JPanel();
+ private JPanel maxColour = new JPanel();
- JPanel jPanel2 = new JPanel();
+ private JCheckBox thresholdIsMin = new JCheckBox();
- BorderLayout borderLayout1 = new BorderLayout();
+ protected static final int MIN_WIDTH = 500;
- private JComboBox<String> threshold = new JComboBox<String>();
+ protected static final int MIN_HEIGHT = 240;
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+ oldgroupColours = new Hashtable<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
}
Desktop.addInternalFrame(frame,
MessageManager.getString("label.colour_by_annotation"), 520,
215);
-
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ useOriginalColours.setSelected(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
seqAssociated.setSelected(acg.isSeqAssociated());
}
- annotations = new JComboBox<String>(
- getAnnotationItems(seqAssociated.isSelected()));
+ Vector<String> annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
+ annotations = new JComboBox<>(annotItems);
populateThresholdComboBox(threshold);
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- annotations.setSelectedItem(acg.getAnnotation());
+ String label = getAnnotationMenuLabel(acg.getAnnotation());
+ annotations.setSelectedItem(label);
switch (acg.getAboveThreshold())
{
case AnnotationColourGradient.NO_THRESHOLD:
getThreshold().setSelectedIndex(2);
break;
default:
- throw new Error(
- MessageManager
- .getString("error.implementation_error_dont_know_about_thereshold_setting"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_about_threshold_setting"));
}
- thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+ thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
}
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- }
+ jbInit();
adjusting = false;
updateView();
frame.pack();
}
- public AnnotationColourChooser()
+ @Override
+ protected void jbInit()
{
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ super.jbInit();
- private void jbInit() throws Exception
- {
minColour.setFont(JvSwingUtils.getLabelFont());
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
}
}
});
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
+
+ defColours = new JButton();
defColours.setOpaque(false);
defColours.setText(MessageManager.getString("action.set_defaults"));
defColours.setToolTipText(MessageManager
@Override
public void actionPerformed(ActionEvent arg0)
{
- resetColours_actionPerformed(arg0);
+ resetColours_actionPerformed();
}
});
- annotations.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- getThreshold().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed(e);
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- currentColours.setFont(JvSwingUtils.getLabelFont());
- currentColours.setOpaque(false);
- currentColours.setText(MessageManager
- .getString("label.use_original_colours"));
- currentColours.addActionListener(new ActionListener()
+ useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+ useOriginalColours.setOpaque(false);
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
+ useOriginalColours.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- currentColours_actionPerformed(e);
+ originalColours_actionPerformed();
}
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- thresholdIsMin_actionPerformed(actionEvent);
+ thresholdIsMin_actionPerformed();
}
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
+ seqAssociated
+ .setText(MessageManager.getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+ seqAssociated_actionPerformed(annotations);
}
});
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
+ JPanel jPanel2 = new JPanel();
jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
jPanel1.add(cancel);
jPanel2.add(annotations, "grow, wrap");
jPanel2.add(seqAssociated);
- jPanel2.add(currentColours);
+ jPanel2.add(useOriginalColours);
JPanel colpanel = new JPanel(new FlowLayout());
colpanel.setBackground(Color.white);
colpanel.add(minColour);
this.validate();
}
- protected void resetColours_actionPerformed(ActionEvent arg0)
+ protected void resetColours_actionPerformed()
{
setDefaultMinMax();
updateView();
private void setDefaultMinMax()
{
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
}
public void minColour_actionPerformed()
updateView();
}
+ @Override
public void reset()
{
- av.setGlobalColourScheme(oldcs);
+ this.ap.alignFrame.changeColour(oldcs);
if (av.getAlignment().getGroups() != null)
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg.cs = oldgroupColours.get(sg);
+ sg.setColourScheme(oldgroupColours.get(sg));
}
}
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
{
- if (currentColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
updateView();
}
getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
- public JComboBox<String> getThreshold()
+ public void originalColours_actionPerformed()
{
- return threshold;
- }
-
- public void setThreshold(JComboBox<String> threshold)
- {
- this.threshold = threshold;
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
+ boolean selected = useOriginalColours.isSelected();
+ if (selected)
{
reset();
}
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
+ maxColour.setEnabled(!selected);
+ minColour.setEnabled(!selected);
+ thresholdIsMin.setEnabled(!selected);
updateView();
}
return;
}
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]]);
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
+ thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
&& getCurrentAnnotation().threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
-
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ float range = getCurrentAnnotation().graphMax * ONETHOUSAND
+ - getCurrentAnnotation().graphMin * ONETHOUSAND;
+
+ slider.setMinimum(
+ (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+ slider.setMaximum(
+ (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+ slider.setValue(
+ (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
}
- colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
+ colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
}
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (useOriginalColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+
+ this.ap.alignFrame.changeColour(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+ sg.setColourScheme(
+ acg.getInstance(av, sg));
+ }
+ }
+ }
+
+ @Override
+ protected void sliderDragReleased()
+ {
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
+ }
}
git://source.jalview.org / jalview.git / blobdiff